Download The Origins of Variation

The Origins of Variation
The Cell Cycle
Interphase
G1 – gap or growth 1
S – synthesis
G2– gap or growth 2
Mitosis – karyokinesis and cytokinesis
Prophase – condensation
Metaphase – chromosomes at equatorial plane
Anaphase – chromosomes separate
Telophase – decondensation
cytokinesis
Meiosis
defines “sexual reproduction” (even in parthenogenic species)
two consecutive reduction divisions
chromosome replication already occurred during S phase of
interphase
differences in meiosis and mitosis occur during in prophase
increases genetic variation through recombination
Prophase I
Leptotene – condensation
Zygotene – homologous chromosomes pair (synapsis) to form
tetrad of 4 chromatids (two diploid chromosomes)
Pachytene – crossing over occurs, complement is now haploid
because each chromatid is now unique even though still joined to
another at the centromere
Diplotene – paired chromosomes begin to separate, cross-overs are
visible as chiasmata
Diakinesis – separation of maternal and paternal homologs
complete in places, producing dyads
but the segregation and assortment of maternal and paternal
dyads is random
Prophase II
dyads split as individual chromatids
chromatids again segregate and assort independently
Interphase
Meiosis
two mechanisms of recombination in meiosis
crossing over - the exchange of genetic material between
chromosomes of different parental origin, during synapsis
(in Prophase I) of meiosis;
a minimum of at least one exchange of chromosomal
arms between non-sister chromosomes in each tetrad
independent assortment - a unique mixture of
chromatids of maternal, paternal, and recombined
chromatids in each gamete
Origins of Genetic Variation
1) mutation - an alteration in DNA sequence, various types
2) intragenic recombination - results in entirely new
associations of genes not present in either parental genome
Two forms of intragenic recombination:
a) crossing over
b) independent assortment
3) reticulation – acquisition of genetic material from unrelated
or relatively unrelated sources (e.g., hybrid species, horizontal
gene transfer)
General Types of Mutations
1) point mutations
2) chromosomal rearrangements and chromosomal number
variation
The “Central Dogma”
Transcription – polymerization of mRNA from ssDNA
template
Translation – tRNA- and ribosome-mediated
polymerization of amino acids from mRNA template
Point Mutation
redundancy of genetic code - 64 combinations of nucleotide
triplets (codons) but only 22 amino acids in living organisms
(selenocysteine is a post-transcriptionally modified from UGA
codon; pyrrolysine genetically coded in methanogenic Archaea)
synonymous vs nonsynonymous substitution
missense mutation – change in amino acid translation
nonsense mutation – results in premature stop codon
Redundancy of genetic code
1st position - intermediate translational effect
2nd position - large translational effect
3rd position - almost never a translational effect
Vertebrate Mitochondrial Genetic Code (others exist)
Point Mutation = nucleotide substitution or
single nucleotide polymorphisms (SNPs)
1.3% of human genome (36.8 million total)
transition C  T, A  G little effect on translation, common
transversion purine  pyrimidine, big effect on translation,
uncommon
both spontaneous deamination and error in replication of
methylated cytosine  thymine (the most common
nucleotide substitution, especially in hypermutation of sex
chromosomes)
Mutation Rate = μ (substitution rate)
μ = 10-8/locus/generation in human nuclear genome
μ = 10-5/locus/generation in human mitochondrial genome
μ = up to 10-3/locus/generation in some viruses
in humans, at least 1 new phenotypically distinct mutant per
gamete per generation
>120 point mutations per human
A typical genome differs from the reference human genome at 4.1
to 5.0 million sites
99.9% of variants consist of SNPs and short insertions/deletions
implications of mutation rate on molecular clock
apparent mutation rate is based only on substitutions that persist
in the genome
mutations that occur at nucleotide positions that affect
phenotype (nonsynonymous) may be eliminated by selection
selection, speciation, population size, or other factors may
accelerate or retard the molecular clock
to the extent that the molecular clock is a good time-keeper,
recent lungfishes are hypothetically as different genetically from
Devonian lungfishes as humans are from Devonian lungfishes
other types of mutations - Chromosomal
Rearrangements or Structural Variants (SV)
fusion and fission - so large that they can be appreciated under a
microscope
chromosomal rearrangements may include centromeres, which may
result in their loss or doubling on rearranged chromosomes and
ultimately to loss or destruction of the chromatid through
nondisjunction (failure of chromatids to segregate during diakinesis)
Metacentric chromosome - symmetrical arms
Acrocentric chromosome - long and short arms
Robertsonian Rearrangements - conversion from metacentric
to/from acrocentric by fusion or fission
Chromosomal Duplication
e.g., autopolyploidy, Down’s syndrome (trisomy 21), Klinefelter’s
syndrome (XXY)
Insertions and Deletions (“Indels”)
the addition or removal of DNA sequence to a chromosome
range in size from one nucleotide to thousands
mechanisms of insertion/deletion:
a) replication slippage – usually mono-, di- tri-nucleotide repeats
that causes DNA polymerase enzyme to ‘slip’ and add or delete
a repeat; form hotspots of length variation - microsatellite
alleles (also known as STRs [single tandem repeats] and SSRs)
b) mispairing during synapsis followed by unequal crossing over or
repair
c) mobile genetic elements
Role of Indels
frameshift mutation - change in open reading frame (ORF) of
translation due to insertion or deletion (that is not a multiple of
3 nucleotides) within a protein coding gene; results in missense
mutation of all downstream codons
non-frameshift mutant allele causative agents of disease
e.g., cystic fibrosis, Huntington’s disease, fragile X syndrome
reduced recombination in heterogametic sex chromosomes
in viruses and bacteria - roles in immunoevasion and
cytoadherance, fusion protein expression
Translocation and Transposition
movement of DNA sequences to new locations
Mobile Genetic Elements
Insertion sequences - small, include only transposase gene
(mostly prokaryotes only)
Transposons
also:
Integrating Plasmids or “Episomes”
Bacteriophages
Group II Introns – self-catalyzing ribozymes
Transposons
Class I (“Retrotransposons” or “retroelements”)
include reverse transcriptase gene
“copy and paste” DNA  RNA  DNA
very large and may include additional genes or parts thereof
comprise large percentages of the genome of many organisms
~42% of human genome, ~90 of wheat genome
Types:
Viral, with long terminal repeats (LTRs)
Long Interspersed Nuclear Elements (LINEs) or non-LTR viral
retrotransposons, at least 21% of human genome
e.g., LINE-1 active in human genome, 6kb, implicated in
epithelial cell carcinoma, schizophrenia
Short Interspersed Nuclear Elements (SINEs), nonviral
e.g., Alu I repeat ~300 bp, ~1,500,000 copies, ~10.7-13% of
human genome, classically referred to as ‘selfish DNA’
Transposons
Class II (“DNA Transposons”)
include transposase gene
“cut and paste” short direct repeats followed by inverted repeats
large and may include additional genes
Role of Transposons (Classes I and II)
Duplicative or Replicative Transposition
e.g., believed to have been the vehicle of gene duplication
producing three color receptors in primate retina
in DNA Transposons – may result in gene duplication during Sphase of interphase when donor has been replicated but target
site has not
in Retrotransposons – simply by repeated replication
Role of Transposons, continued
Disrupt gene function thru frameshift of open reading frame
(ORF) of protein coding gene or translocation of gene to another
chromosome
e.g., colorectal cancer, breast cancer, Ewing’s sarcoma,
hypercholesterolemia, hemophilia, neurofibromatosis, diabetes
mellitus type 2
hypothetically regulatory
e.g., Alzheimer’s syndrome, lung cancer, gastric cancer
Permanent Translocation Heterozygosity or “meiotic chains” non-independent segregation of chromosomes in meiosis
mediated by pairing of homologous segments in different
chromosomes, mostly in plants, some invertebrates, and
monotreme mammals
vehicle of Horizontal Gene Transfer (HGT)
Still more chromosomal rearrangements
Inversion - the flipping over (reverse orientation) of a DNA
sequence
one example known to have produced increased fertility in
women
Pericentric inversion – includes centromere
Paracentric inversion – does not include centromere
Unequal crossing over involving pericentric inversions result in
centromere loss in one chromosome, but gain in the other
which in turn may result in:
nondisjunction (failure of homologous chromosomes to
segregate) and aneuploidy (incorrect number of
chromosomes per gamete, and/or
chromosomal fission
Still more chromosomal rearrangements
Duplication or Copy Number Variation (CNV) - mispairing during
meiotic synapsis followed by unequal crossing over
12%-19% of human genome (possibly as much as 50%) – much
more than SNPs (only 1.3% of genome)
May have strong phenotypic effects! (at least 40 diseases)
Potential fates of gene duplications
multicopy genes
defunctionalization - pseudogenes
neofunctionalization - multigene families
e.g., globin gene family
addition or deletion of repeats
humans have >1,750 duplicated genes compared with chimps
Orthology – strictly homologous single-copy genes
Paralogy – duplicated genes; between species these share common
ancestry that predates population or species divergence
Still more chromosomal rearrangements
Conversion - mispairing during meiotic synapsis followed by
repair, two mechanisms:
Double Holliday Junction (DHJ) – dsDNA exchange during
synapsis
Synthesis Dependent Strand Annealing (SDSA) – information
exchange only
may result in concerted evolution of multicopy genes or
repeated elements
Holliday Junction
a secondary structure formed between 4 DNA strands
its role in recombination
Reticulation
acquisition of genetic material from unrelated or relatively
unrelated sources
Hybridization
Horizontal or Lateral Gene Transfer (HGT or LGT)
Hybridization (interspecific)
Potential outcomes
species fusion - the formation of hybrid species, usually
allopolyploids but sometimes homoploids; after a few
generations the genomes of the parental species become
thoroughly mixed by crossing over and fusions and fissions
e.g., many angiosperms
e.g., red wolf
introgression (introgressive hybridization) - gene flow or "leaking"
of genes of one species into another by way of backcrossing
hybrid offspring to parental types, i.e., movement of genetic
material from one population to another by sexual reproduction
e.g., movement of mitochondrial genome of one species into
another
e.g., acquisition of genetically engineered genes (e.g., pest or
pesticide resistance, frost tolerance) from crop plants into weed
species
HGT (LGT)
the insertion of retroelements and exogenous transposons into a
genome
the translocation of genetic material between endosymbionts and
their hosts or by bacteriophage vectors
e.g., mitochondria - endosymbiotic origin, evidence from cell
membranes, gene structure, origin of replication, the fact that
mitochondrial rRNAs are more similar to endosymbiotic
bacterial (Rickettsia) rRNAs than to nuclear rRNAs of
eukaryotes, and ongoing movement of genetic material from
mitochondria (and chloroplast) genomes to the nuclear
genome (numt's) resulting in obligate endosymbiosis
e.g., plasmids in bacteria - genetic piracy of advantageous genes
(e.g., antibiotic resistance) by restriction endonucleases
HGT (LGT)
e.g., genome of house mouse - more than 50% retroviral in origin
e.g., endogenous retroviruses (ERVs) - expressed during
implantation in placental mammals, act as immunodepressors
and create a syncytium around the developing embryo within
the uterine endometrium
e.g., bacterial biofilms – up to 30% of bacterial genomic diversity
may be extracellular, and taken up by bacteria
e.g., obligate insect bacterial endosymbionts – e.g., protists in
termites involved in digestion or nutrient production
e.g., photosynthetic zooxanthellae in corals
Epilogue: A typical genome differs from the reference human
genome at 4.1 to 5.0 million sites
99.9% of variants consist of SNPs and short indels (insertions/deletions)
2,100 to 2,500 structural variants, including:
1,000 large deletions
160 copy-number variants (CNVs)
915 Alu I insertions
128 LINE 1 insertions
51 SVA (SINE variable number tandem repeat Alu) insertions
4 NUMTs (nuclear mitochondrial DNA fragments)
10 inversions
- affecting 20 million bases of sequence